MethBat outliers, Mimvir/Gicam scores, long reads seq. badges and more

[4.108]

Added

• Gene-overlapping variants shown also for STRs (#5977)
• Case and variant-specific information on ACMG page and PDF export (#5978)
• Allow bypassing the confirmation prompt for the delete rna command via a new --yes option (#5982)
• Parse phasing information and store on genotype call (#5988)
• Link to GTEx for gene, from gene and variant pages (#5995)
• Parse STRdrop details where available (#5991)
• Incomplete penetrance badge, according to HPO (#6008)
• Support for additional variant scoring systems: MivmirScore, GicamScore (#5970)
• Parse and display MivmirExplanation key/values on variant page, when available (#6011)
• Display inheritance models on structural variantS pages (#6015)
• Analysis types wgs-lr and panel-lr (#6029)
• Option to specify database name for the loqusdb API in the scout config file (#6028)
• Allowing filtering cases by type of analysis (advanced options) (#6045)
• Methylation outliers from LRS MethBat from Nallo as omics variants (#5993)
• An ACMG sandbox link included in the main dropdown, pointing to a blank classification page to be used to test the algorithm (#5983)

Changed

• Institutes are now ordered alphabetically by display name on gene panels search (#5965)
• Display all available individual/sample IDs for a case (display_name, individual_id and subject_id) directly on cases page (#5966)
• Revert search of genes in panels. Now search is NOT limited to user's institutes panels any more (#5974)
• Name for Gens buttons: CN profile to Gens(#5985)
• On variants filters form, sort gene panels alphabetically and mark panels that don't belong to the case's clinical panels with asterisk (#5981)
• External links at the bottom of variant page are now ordered alphabetically (#6024)
• Mivmir score explanations sorted by descending value, from the biggest contributor to the smallest (#6058)
• The ACMG classification documentation now more clearly explains about modifications not in Richards et al (#6065)

Fixed

• Do not try to save an ACMG classification when user provided no criteria (#4962)
• When dismissing variants from variantS page, reloaded page remembers variant selection position (#5969)
• Smaller PDFs exported from ACMG classification page (#5976 and #6054)
• When adding a germline variant to a ClinVar submission, make sure it ends up in a germline submission (#5990)
• Invalid scroll_pos handling in variants view (#5999 and #6022)
• Native type hint of iterable with subtype not compatible with python 3.11 (#6007)
• Error in parsing reduced penetrance from HPO genes to phenotypes (#6004)
• Top left SNVs button on omics outliers page (#6001)
• Omics variants RNA sashimi button locus generation does not follow RNA genome build (#6002)
• HGVSp display encoding on gene-variants (SNV and SVs) page (#6018)
• RefSeq transcripts panel on variant page, which was missing RefSeq ID and links for some transcripts (#6027, #6031)
• Phenotype_terms empty crash on case page (#6034)
• Updated supercharge/mongodb-github-action to v1 (1.12.1) in order to fix automatic tests failing with "client too old → daemon too new" error before even starting (#6043,#6044)
• On Local Observations panels, set number of homozygous observations to 0 and not N/A if Nr obs. is 0 (#6038)
• Color case LR badges (#6050)
• Make sorting of gene panels containing a gene case-insensitive (#6052 and #6056)
• Make sorting of institutes case-insensitive on new user form, dashboard and institute settings (#6061, #6062)
• Cases page crashing due to missing analysis date when a case is loaded using VCF + ped file (#6067)
• Add user dropdown selects visible in dark mode (#6068)
• Fixed links to Ensembl and NCBI transcripts from main Transcripts and Protein panel on variant page (#6041)
• Methbat methylation Uncategorized icon display (#6074)
• General report page timeout when case has dozens of dismissed variants - show only the first 15 (#6035)
• Fixed displaying dismissed MEIs and cancer SVs on general case report (#6077)